Showing : Genomicranges • reset
1
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How to make combined annotation of 5'UTRs and CDS's?
annotation concatenation GRangesList GenomicRanges
6.5 years ago anmej • 0
0
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2
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1.2k
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feel confused when identifying overlapping regions by intersect method
GenomicRanges overlaps intersect
updated 6.5 years ago by ★ 11k • written 6.5 years ago by • 0
2
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1
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1.7k
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Create a matrix to show overlaps among multiple GRanges
r GRanges GenomicRanges
updated 6.5 years ago by 68k • written 6.5 years ago by ▴ 40
6
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8
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3.8k
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Ranges from a fasta file
biostrings fasta genomicranges granges
updated 6.6 years ago by 25k • written 6.6 years ago by ▴ 90
6
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12
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2.7k
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mclapply to loop over a GRangesList object
GenomicRanges GRanges GRangesList parallel mclapply
6.6 years ago foehn ▴ 100
0
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4
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2.3k
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Unexpected behaviour of set operations on GRanges objects when dplyr is loaded
GenomicRanges S4Vectors dplyr
updated 6.7 years ago by 68k • written 6.7 years ago by ▴ 140
2
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2
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2.7k
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Error in installation of scran
S4Vectors IRanges XVector GenomicRanges scran
updated 6.7 years ago by ★ 29k • written 6.7 years ago by • 0
4
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2
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1.5k
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Speed efficient way to select the n-th element from GRangsList
R GenomicRanges IRanges
6.7 years ago foehn ▴ 100
0
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1
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1.0k
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How is it possible to override the constructor of the GRanges class?
genomicranges granges
6.7 years ago Shaurya Jauhari • 0
5
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8
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11k
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Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 3.6 years ago by • 0 • written 10.0 years ago by ▴ 50
0
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1
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1.6k
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Subset bam file in R
rsamtools genomicalignments genomicranges
updated 6.8 years ago by ★ 11k • written 6.8 years ago by • 0
2
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1
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1.4k
views
Bug in follow and precede
software error genomicranges iranges
updated 6.8 years ago by ★ 6.8k • written 6.8 years ago by • 0
1
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2
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3.5k
views
How to convert bedgraph to wig
rtracklayer genomicranges
updated 6.8 years ago by ★ 11k • written 6.8 years ago by • 0
0
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7
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1.7k
views
rtracklayer cannot export empty BED file
rtracklayer bed genomicranges
updated 6.8 years ago by ★ 11k • written 6.8 years ago by ▴ 100
1
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1
reply
901
views
Bug report for GenomicRanges
genomicranges
updated 6.8 years ago by ★ 11k • written 6.8 years ago by ▴ 170
7
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5
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4.8k
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summarize scores of GRanges into bins
genomicranges grangeslist bin findoverlaps
updated 6.9 years ago by • 0 • written 8.0 years ago by ★ 1.5k
0
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1
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815
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How to find overlaps in genomic sequences comparing patients to themselves
genomicranges
6.9 years ago sbailey5 • 0
0
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2
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1.3k
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Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
6.9 years ago A ▴ 60
0
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3
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1.6k
views
GenomicRanges based on indices or more conditions, and add column from match
genomicranges iranges findoverlaps
6.9 years ago francesca casalino ▴ 50
2
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1
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1.3k
views
Intra-range transformation on GPos-objects?
genomicranges gpos granges
updated 6.9 years ago by 16k • written 7.0 years ago by ▴ 180
0
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0
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1.7k
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GenomicFeatures: How to extract a gene's upstream region of TSS up to the end position of the flanking (nearby) gene.
genomicranges genomicfeatures promoter upstream_flank
7.0 years ago Wojeff • 0
2
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2
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5.0k
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Concatenate a list of genomic ranges
r granges genomicranges
updated 7.0 years ago by 68k • written 7.0 years ago by • 0
0
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2
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962
views
Error: the "phase" metadata column must contain 0, 1, or 2, for all the CDS features
genomicranges
7.1 years ago bbrink • 0
3
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3
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1.7k
views
Gaia results including negative widths
gaia genomicranges iranges
updated 7.1 years ago by ▴ 40 • written 7.1 years ago by ▴ 10
1
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1
reply
3.1k
views
Extracting gene structures from a GFF3 file for use with annotateWithGeneParts()
genomicfeatures genomation genomicranges methylation annotation
updated 7.1 years ago by ▴ 20 • written 7.1 years ago by • 0
0
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3
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1.4k
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Nearest genomic ranges and distances in circular ranges
genomicranges
updated 7.1 years ago by ★ 6.8k • written 7.1 years ago by • 0
0
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3
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990
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'downstream' disappeared from GenomicRanges package?
genomicranges
7.2 years ago Vang Le ▴ 80
3
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2
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1.4k
views
Simplifying a RaggedExperiment using qreduceAssay and weighted means.
raggedexperiment genomicranges
updated 7.2 years ago by 25k • written 7.2 years ago by ★ 1.1k
5
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4
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2.7k
views
How do I do a bedtools like intersection in GenomicRanges?
genomicranges
updated 7.2 years ago by ★ 11k • written 7.2 years ago by ▴ 40
2
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12
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2.6k
views
nearest without overlapping
genomicranges
updated 7.2 years ago by 16k • written 7.2 years ago by ▴ 40
1
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5
replies
3.5k
views
Replacement for lapply on a GRanges?
genomicranges
updated 7.3 years ago by 16k • written 7.3 years ago by ▴ 890
7
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5
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2.5k
views
Strange error in bsseq when trying to assign seqinfo
bsseq genomeinfodb genomicranges seqinfo
written 7.3 years ago by ▴ 140
0
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1
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1.5k
views
GenomicRanges distanceToNearest: trouble replicating snp-gene mapping from older version
GenomicRanges distancetonearest strandedness
updated 7.4 years ago by ★ 6.8k • written 7.4 years ago by • 0
0
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1
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1.2k
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Detect Sites with Minimum Gap in GRanges Object
R genomicranges granges grange
7.4 years ago g.k • 0
2
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2
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1.2k
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Features within 2kb window, but with resampling
genomicranges granges slidingwindow
updated 7.5 years ago by ★ 11k • written 7.5 years ago by • 0
3
votes
1
reply
1.0k
views
Finding the nearest n genes from a genomic loci
genomicranges
updated 7.5 years ago by ★ 11k • written 7.5 years ago by ▴ 20
1
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2
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1.6k
views
extending GenomicRanges::reduce warning, why ?
GenomicRanges reduce setMethod setGeneric
updated 7.5 years ago by 25k • written 7.5 years ago by ▴ 80
1
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3
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2.0k
views
How to operate on circular sequences with GenomicRanges?
GenomicRanges mitochondria circular
updated 7.5 years ago by ★ 6.8k • written 7.5 years ago by ▴ 120
3
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2
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2.4k
views
coverage() output SimpleRleList cannot be converted to GRanges
bug genomicranges granges rlelist coverage
updated 7.6 years ago by 16k • written 7.6 years ago by ▴ 10
0
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5
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1.4k
views
Problem converting annotation to GenomicRanges object
genomicranges
7.6 years ago Anton01 • 0
3
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4
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1.6k
views
Future plans for the new GPos class
genomicranges gpos
updated 7.6 years ago by 16k • written 7.6 years ago by ▴ 180
2
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8
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6.4k
views
GenomicRanges: identify overlapping regions, get intersection between each overlapping pair and add gene coordinates (start, end, strand and ids)
genomicranges overlap intersect findoverlaps
7.6 years ago Caroline Grisbach Meissner ▴ 10
2
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3
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1.8k
views
GRanges object from gene list
granges bed genomicranges genomeintervals deseq2
7.6 years ago rbronste ▴ 60
2
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4
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2.0k
views
Make window around TSS and get values from another data.frame for bins of the specified window
R granges genomicranges chipseq
updated 7.7 years ago by ★ 11k • written 7.7 years ago by ▴ 20
0
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0
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1.1k
views
coverage no longer works on GPos objects?
genomicranges gpos
7.7 years ago maltethodberg ▴ 180
1
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4
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4.3k
views
Generate 3' UTR and 5' UTR ranges from a gff file
gff genomicranges
updated 7.7 years ago by ★ 11k • written 7.7 years ago by ▴ 10
0
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6
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4.7k
views
GRanges::distanceToNearest does not return distance to nearest
granges genomicranges
updated 7.7 years ago by ★ 6.8k • written 7.8 years ago by ▴ 40
0
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1
reply
1.5k
views
Error when subsetting a RaggedExperiment by GenomicRanges
raggedexperiment genomicranges
updated 7.7 years ago by 700 • written 7.7 years ago by • 0
0
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1
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1.7k
views
GenomicRanges fails to load due to missing ngap method
software error genomicranges loadnamespace
updated 7.8 years ago by 25k • written 7.8 years ago by • 0
0
votes
2
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1.2k
views
GRangesList: wiered error
genomicranges genomicfeatures
7.8 years ago Fabian Grammes ▴ 20
403 results • Page 3 of 9
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Comment: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi by ATpoint ★ 4.9k
Not that this is a good way of doing it, but if I have single-cell data and the gut feeling that methods disagree a lot then I usually run …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by games • 0
The error occurs because accession A0A287BB68 is not in the org.Ss.eg.db database, so AnnotationDbi::select() cannot identify a valid key. …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by games • 0
The error occurs because accession A0A287BB68 is not in the org.Ss.eg.db database, so AnnotationDbi::select() cannot identify a valid key. …
Comment: org.Ss.eg.db MAMDC4 maps to incorrect UNIPROT key by thundernight • 0
I'm actually having the same problem. [Spanish dictionary][1] [1]: https://spanishdictionary.cc
Comment: voomLmFit fitted log-CPM values by Gordon Smyth 53k
The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…
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